Summary information and primary citation

PDB-id
6jq6; DSSR-derived features in text and JSON formats
Class
RNA
Method
X-ray (2.626 Å)
Summary
Hatchet ribozyme structure soaking with ir(nh3)6+
Reference
Zheng L, Falschlunger C, Huang K, Mairhofer E, Yuan S, Wang J, Patel DJ, Micura R, Ren A (2019): "Hatchet ribozyme structure and implications for cleavage mechanism." Proc.Natl.Acad.Sci.USA, 116, 10783-10791. doi: 10.1073/pnas.1902413116.
Abstract
Small self-cleaving ribozymes catalyze site-specific cleavage of their own phosphodiester backbone with implications for viral genome replication, pre-mRNA processing, and alternative splicing. We report on the 2.1-Å crystal structure of the hatchet ribozyme product, which adopts a compact pseudosymmetric dimeric scaffold, with each monomer stabilized by long-range interactions involving highly conserved nucleotides brought into close proximity of the scissile phosphate. Strikingly, the catalytic pocket contains a cavity capable of accommodating both the modeled scissile phosphate and its flanking 5' nucleoside. The resulting modeled precatalytic conformation incorporates a splayed-apart alignment at the scissile phosphate, thereby providing structure-based insights into the in-line cleavage mechanism. We identify a guanine lining the catalytic pocket positioned to contribute to cleavage chemistry. The functional relevance of structure-based insights into hatchet ribozyme catalysis is strongly supported by cleavage assays monitoring the impact of selected nucleobase and atom-specific mutations on ribozyme activity.

Cartoon-block schematics in six views (download the tarball)

PyMOL session file Download PDB file View in 3Dmol.js